Removing ITS and primers from QIAseq 16S/ITS panel using qiime2

[poop_queen]

Hello microbiome enthusiasts!

I have a question regarding processing samples sequenced using the QIAseq 16S/ITS panel. Each person's data consists of one paired fastq file. The sequencing facility suggested using qiime2 + dada2 + silva on these files. However, after reading THIS post I'm concerned this may not be the correct approach. The fastq file supposedly contains ITS, V1V2, V2V3, V3V4, V4V5, V5V7, and V7V9 regions.

I have two specific questions:

1. I am really struggling to conceptualize what is within the fastq file after such a sequencing approach. I've attempted to visualize my current understanding below, but I'm unsure if it's accurate.
   

2. My goal is to eliminate ITS and primers, and classify V1-V9 as a single unit instead of six separate fragments. What's the recommended method for accomplishing this in qiime2?

I apologize if these questions seem basic; I'm relatively new to this area of study. Thank you for any guidance you can provide!

[jwdebelius (Justine Debelius)]

Hi @poop_queen!

Welecome to the :qiime2: forum and what a great name!

This seems like a really good application for Sidle. If you have the primers, Sidle has instructions to split the data into multiple regions and then reconsruct them into a normalized table. It can also help you build a 16S phylogenetic tree if you use Silva 128 as your database. (You can use any database you want if you dont care about phylogeny but it can only do phylogeny for Silva 128).

Best,
Justine